The current load transfer method does not consider the weight of pile shaft itself. When it is directly applied to calculating the settlement of super-long pile in the soft soil area, the computational accuracy can hardly meet the requirements of strict control criteria for post-construction settlement of high-speed railway. This paper considers the settlement calculation of both soil around pile due to dewatering and soil beneath pile tip using tip-resistance elastic model. The calculation method of dewatering-induced foundation pile settlement is proposed by modifying and solving the basic differential equation of load transfer method. The weight of pile shaft is combined. A hypothetic load transfer function of skin friction is included using Kedzi’s model. A case study is given. The theoretical solution and the FEM embedded with the hypothetic load transfer function are used. The skin friction, the shaft axial force and the foundation pile settlement are comparatively analyzed under either the action of upper load or the combined loading of upper load and dewatering. The additional vertical displacement of soil around pile due to foundation pile settlement is obtained using both the FEM and the theoretical calculations. The two results have slight difference. The rationality and correctness of the theoretical calculation are verified since its corresponding laws change almost in the same way as those of FEM.